Hello Everybody, I have 2 different protein chains (not a homodimer), chain C and chain F in a PDB file. These 2 proteins are interacting proteins close in proximity. I would like to use energy minimization (EM) and equilibration (EQ) to approximate the most relaxed interacting conformation between these 2 proteins. However, after EM, these 2 chains become far apart in space. (I checked with PyMOL using editconf for the resulting EM .gro file) My previous EM and EQ run for a different set of 2 proteins did not have this error. May I please know how I can rectify this?
Thank you! - Benjamin
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